E-Clear, the company responsible for online ticket sales at the failed airline Flyglobespan, has been placed into administration.
A High Court judge granted the administration order following a request from PricewaterhouseCoopers (PWC) - FlyGlobespan's administrators.
PWC has accused E-Clear of withholding £35m from the airline before its collapse in December last year.
The administrators said it was now clear the funds were "no longer there".
The funds being disputed consist of payments made by customers for flights, which PWC claims were not passed on to Globespan - FlyGlobespan's parent company, which was based in Edinburgh.
PWC said it had no explanation for why the money had been held back and E-Clear had not told it how much money existed.
A request to put the contested funds into a joint account had also been refused, it said.
Following the decision to place E-Clear into administration, Bruce Cartwright, administrator at PWC, said that the company would be working to recover as much money as possible for Globespan's creditors.
"Those who bought services on credit card or visa debit, that have not been supplied, will continue to be protected by consumer card legislation and should contact their credit card issuer," he added.
Thousands of passengers were stranded abroad and 550 staff made redundant when the FlyGlobespan collapsed in December 2009.
A Scottish Government spokesman said: "This is a deeply worrying situation and we will continue to press the UK Government to investigate fully the circumstances behind the collapse of Globespan".